BuildFeatureMatrix: Build a Feature matrix from the with speaq 2.0 processed data

In speaq2: Wavelet Based Tools for Feature-Wise Analysis and Quantification of Nuclear Magnetic Resonance (NMR) Spectra

Description

This function converts the aligned peak data (so at least pake detection and alignment/grouping has to be completed) to a matrix with features (aligned peaks) in the columns and the value of that peak for every sample in the rows.

Usage

BuildFeatureMatrix(Y.data, var = "peakValue", impute = "zero",
  delete.below.threshold = FALSE, baselineThresh = 500, snrThres = 3,
  thresholds.pass = "any-to-pass")

Arguments

Y.data	The dataset after (at least) peak detection and alignment with speaq 2.0.
var	The variable to be used in the Featurematrix. This can be any of 'peakIndex', 'peakPPM', 'peakValue' (default), 'peakSNR', 'peakScale', or 'Sample'.
impute	What to impute when a certain peak is missing for a certain sample and feature combo. Options are 'zero' (or 'zeros'), any other statement will produce NA's.
delete.below.threshold	Whether to ignore peaks for which the 'var' variable has a value below 'baselineThresh' (default = FALSE).
baselineThresh	The threshold for the 'var' variable peaks have to surpass to be included in the feature matrix.
snrThres	The threshold for the signal-to-noise ratio of a peak.
thresholds.pass	This variable lets users deside whether a peak has to pass all the thresholds (both snrThres and baselineThresh), or just one. (If the peak does not need to surpass any thresholds set 'delete.below.threshold' to FALSE).

Value

a matrix, data.matrix, with samples for rows and features for columns. The values in the matrix are thoes of the 'var' variable.

Author(s)

Charlie Beirnaert, [e-mail]

Examples

## Not run: 
# 'DetectedPeaks_aligned' is the peak data after wavelet based peak detection and alignment
Featurematrix <- BuildFeatureMatrix(Y.data = DetectedPeaks_aligned, var = 'peakValue')

## End(Not run)

speaq2 documentation built on May 6, 2017, 4:09 a.m.